kmerresistance - correlates mapped genes with the predicted species of WGS samples

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

kmerresistance 2.0+git20180205.26467e9              June 2018                                  KMERRESISTANCE(1)

       KmerResistance  correlates mapped genes with the predicted species of WGS samples, where this this allows
       for identification of genes in samples which have been poorly sequenced or high accuracy predictions  for
       samples  with  contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which
       is also freely available.

       Mapping reads against resistance genes:

                kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria

       kmerresistance - correlates mapped genes with the predicted species of WGS samples

-i     Input/query file name                                   REQUIRED

       -o     Output file                                             REQUIRED

       -t_db  Template DB                                             REQUIRED

       -s_db  Species DB                                              REQUIRED

       -id    ID threshhold                   70.0

       -dct   Depth correction threshhold     0.1

       -kma   alternative KMA         kma

   KMAoptions:-i     Input/query file name           None            REQUIRED

       -o     Output file                     None            REQUIRED

       -t_db  Template DB                     None            REQUIRED

       -k     Kmersize                        16

       -e     evalue                          0.05

       -delta Align in pieces of delta        511

       -mem_mode
              Use kmers to choose best template, and save memory       False

       -ex_mode
              Searh kmers exhaustively        False

       -deCon Remove contamination            False

       -dense Do not allow insertions in assembly                     False

       -ref_fsa
              Consensus sequnce will have "n" instead of gaps        False

       -matrix
              Print assembly matrix           False

       -mp    Minimum phred score             30

       -5p    Cut a constant number of nucleotides from the 5 prime.   0

       -Sparse
              Run KmerFinder                  False

       -ID    Minimum ID                      1.0%

       -ss    Sparse sorting (q,c,d)          q

       -shm   Use shared DB made by kma_shm   0 (lvl)

       -swap  Swap DB to disk                 0 (lvl)

       -1t1   Skip HMM                        False

       -boot  Bootstrap sequence              False

       -mrs   Minimum alignment score, normalized to alignment length  0.5

       -reward
              Score for match                 1

       -penalty
              Penalty for mismatch            -2-gapopen
              Penalty for gap opening         -3-gapextend
              Penalty for gap extension       -1-h     Shows this help message